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Bordel S, Martín-González D, Börner T, Muñoz R, Santos-Beneit F. Genome-scale metabolic model of the versatile bacterium Paracoccus denitrificans Pd1222. mSystems 2024; 9:e0107723. [PMID: 38180324 PMCID: PMC10878069 DOI: 10.1128/msystems.01077-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 11/26/2023] [Indexed: 01/06/2024] Open
Abstract
A genome scale metabolic model of the bacterium Paracoccus denitrificans has been constructed. The model containing 972 metabolic genes, 1,371 reactions, and 1,388 unique metabolites has been reconstructed. The model was used to carry out quantitative predictions of biomass yields on 10 different carbon sources under aerobic conditions. Yields on C1 compounds suggest that formate is oxidized by a formate dehydrogenase O, which uses ubiquinone as redox co-factor. The model also predicted the threshold methanol/mannitol uptake ratio, above which ribulose biphosphate carboxylase has to be expressed in order to optimize biomass yields. Biomass yields on acetate, formate, and succinate, when NO3- is used as electron acceptor, were also predicted correctly. The model reconstruction revealed the capability of P. denitrificans to grow on several non-conventional substrates such as adipic acid, 1,4-butanediol, 1,3-butanediol, and ethylene glycol. The capacity to grow on these substrates was tested experimentally, and the experimental biomass yields on these substrates were accurately predicted by the model.IMPORTANCEParacoccus denitrificans has been broadly used as a model denitrifying organism. It grows on a large portfolio of carbon sources, under aerobic and anoxic conditions. These characteristics, together with its amenability to genetic manipulations, make P. denitrificans a promising cell factory for industrial biotechnology. This paper presents and validates the first functional genome-scale metabolic model for P. denitrificans, which is a key tool to enable P. denitrificans as a platform for metabolic engineering and industrial biotechnology. Optimization of the biomass yield led to accurate predictions in a broad scope of substrates.
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Affiliation(s)
- Sergio Bordel
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Valladolid, Spain
- />Institute of Sustainable Processes, Valladolid, Spain
| | - Diego Martín-González
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Valladolid, Spain
- />Institute of Sustainable Processes, Valladolid, Spain
| | - Tim Börner
- HES-SO Valais/Wallis, School of Engineering, Institute of Life Technologies, Sion, Switzerland
| | - Raúl Muñoz
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Valladolid, Spain
- />Institute of Sustainable Processes, Valladolid, Spain
| | - Fernando Santos-Beneit
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Valladolid, Spain
- />Institute of Sustainable Processes, Valladolid, Spain
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Palmer M, Steenkamp ET, Coetzee MPA, Blom J, Venter SN. Genome-Based Characterization of Biological Processes That Differentiate Closely Related Bacteria. Front Microbiol 2018; 9:113. [PMID: 29467735 PMCID: PMC5808187 DOI: 10.3389/fmicb.2018.00113] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 01/17/2018] [Indexed: 12/21/2022] Open
Abstract
Bacteriologists have strived toward attaining a natural classification system based on evolutionary relationships for nearly 100 years. In the early twentieth century it was accepted that a phylogeny-based system would be the most appropriate, but in the absence of molecular data, this approach proved exceedingly difficult. Subsequent technical advances and the increasing availability of genome sequencing have allowed for the generation of robust phylogenies at all taxonomic levels. In this study, we explored the possibility of linking biological characters to higher-level taxonomic groups in bacteria by making use of whole genome sequence information. For this purpose, we specifically targeted the genus Pantoea and its four main lineages. The shared gene sets were determined for Pantoea, the four lineages within the genus, as well as its sister-genus Tatumella. This was followed by functional characterization of the gene sets using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. In comparison to Tatumella, various traits involved in nutrient cycling were identified within Pantoea, providing evidence for increased efficacy in recycling of metabolites within the genus. Additionally, a number of traits associated with pathogenicity were identified within species often associated with opportunistic infections, with some support for adaptation toward overcoming host defenses. Some traits were also only conserved within specific lineages, potentially acquired in an ancestor to the lineage and subsequently maintained. It was also observed that the species isolated from the most diverse sources were generally the most versatile in their carbon metabolism. By investigating evolution, based on the more variable genomic regions, it may be possible to detect biologically relevant differences associated with the course of evolution and speciation.
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Affiliation(s)
- Marike Palmer
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Emma T Steenkamp
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Martin P A Coetzee
- Department of Genetic, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Stephanus N Venter
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
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Zhang X, Liu H, Yang F, Yang J, Xue Y, Dong J, Sun L, Yang G, Zhu J, Chu Y, Jin Q. Comparative genome analysis of deleted genes in Shigella flexneri 2a strain 301. Sci Bull (Beijing) 2013. [DOI: 10.1007/bf03325661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Yu C, Li Y, Xia B, Jin C. Solution structure of the cryptic mannitol-specific phosphotransferase enzyme IIA CmtB from Escherichia coli. Biochem Biophys Res Commun 2007; 362:1001-6. [PMID: 17803963 DOI: 10.1016/j.bbrc.2007.08.102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2007] [Indexed: 11/16/2022]
Abstract
The bacterial phosphoenolpyruvate-dependent sugar phosphotransferase system (PEP-PTS) is essential in the coupled transportation and phosphorylation of various types of carbohydrates. The CmtAB proteins of Escherichia coli are sequentially similar to the mannitol-specific phosphotransferase MtlA. The CmtB protein corresponds to the phosphotransferase enzyme IIA component. Here we report the solution structure of CmtB from E. coli at high resolution by NMR spectroscopy. The results show that CmtB adopts a globular fold consisting of a central mixed five-strand beta-sheet flanked by seven helices at both sides. Structural comparison with the IIA domain of MtlA (IIAMtl) reveals high overall similarity, while notable conformational differences at the active site are observed. The active site pocket of CmtB appears to be wider, and the hydrophobic regions around it is larger compared to IIAMtl. Further, the essential arginine residue at the active site of IIAMtl is substituted by a serine in CmtB. Instead, the active pocket of CmtB contains another arginine at a distinct position, suggesting different molecular mechanisms for phosphoryl transfer.
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Affiliation(s)
- Caifang Yu
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China
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Abstract
Escherichia coli and Salmonella enterica serovar Typhimurium exhibit a remarkable versatility in the usage of different sugars as the sole source of carbon and energy, reflecting their ability to make use of the digested meals of mammalia and of the ample offerings in the wild. Degradation of sugars starts with their energy-dependent uptake through the cytoplasmic membrane and is carried on further by specific enzymes in the cytoplasm, destined finally for degradation in central metabolic pathways. As variant as the different sugars are, the biochemical strategies to act on them are few. They include phosphorylation, keto-enol isomerization, oxido/reductions, and aldol cleavage. The catabolic repertoire for using carbohydrate sources is largely the same in E. coli and in serovar Typhimurium. Nonetheless, significant differences are found, even among the strains and substrains of each species. We have grouped the sugars to be discussed according to their first step in metabolism, which is their active transport, and follow their path to glycolysis, catalyzed by the sugar-specific enzymes. We will first discuss the phosphotransferase system (PTS) sugars, then the sugars transported by ATP-binding cassette (ABC) transporters, followed by those that are taken up via proton motive force (PMF)-dependent transporters. We have focused on the catabolism and pathway regulation of hexose and pentose monosaccharides as well as the corresponding sugar alcohols but have also included disaccharides and simple glycosides while excluding polysaccharide catabolism, except for maltodextrins.
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Affiliation(s)
- Christoph Mayer
- Fachbereich Biologie, Universität Konstanz, 78457 Konstanz, Germany
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Reizer J, Paulsen IT, Reizer A, Titgemeyer F, Saier MH. Novel phosphotransferase system genes revealed by bacterial genome analysis: the complete complement of pts genes in mycoplasma genitalium. MICROBIAL & COMPARATIVE GENOMICS 2001; 1:151-64. [PMID: 9689210 DOI: 10.1089/mcg.1996.1.151] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete sequence of the Mycoplasma genitalium chromosome has recently been determined. We here report analyses of the genes encoding proteins of the phosphoenolpyruvate:sugar phosphotransferase system, PTS. These genes encode (1) Enzyme I, (2) HPr, (3) a glucose-specific Enzyme IICBA, (4) an inactive glucose-specific Enzyme IIB, lacking the active site cysteyl residue, and (5) a fructose-specific Enzyme IIABC. Some of the unique features of these genes and their enzyme products are as follows. (1) Each of the genes is encoded within a distinct operon. (2) Both Enzyme I and HPr have basic isoelectric points. (3) The glucose-specific Enzyme IIC bears a centrally located, hydrophilic, 200 amino acyl residue insert that lacks sequence similarity with any protein in the current database. (4) The fructose-specific Enzyme II has a domain order (IIABC), different from those of previously characterized fructose permeases, and its IIA domain more closely resembles the IIANtr protein of Escherichia coli than other fructose-specific IIA domains. The potential significance of these novel features is discussed.
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Affiliation(s)
- J Reizer
- Department of Biology, University of California at San Diego, La Jolla, USA
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McClelland M, Florea L, Sanderson K, Clifton SW, Parkhill J, Churcher C, Dougan G, Wilson RK, Miller W. Comparison of the Escherichia coli K-12 genome with sampled genomes of a Klebsiella pneumoniae and three salmonella enterica serovars, Typhimurium, Typhi and Paratyphi. Nucleic Acids Res 2000; 28:4974-86. [PMID: 11121489 PMCID: PMC115240 DOI: 10.1093/nar/28.24.4974] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Escherichia coli K-12 genome (ECO) was compared with the sampled genomes of the sibling species Salmonella enterica serovars Typhimurium, Typhi and Paratyphi A (collectively referred to as SAL) and the genome of the close outgroup Klebsiella pneumoniae (KPN). There are at least 160 locations where sequences of >400 bp are absent from ECO but present in the genomes of all three SAL and 394 locations where sequences are present in ECO but close homologs are absent in all SAL genomes. The 394 sequences in ECO that do not occur in SAL contain 1350 (30.6%) of the 4405 ECO genes. Of these, 1165 are missing from both SAL and KPN. Most of the 1165 genes are concentrated within 28 regions of 10-40 kb, which consist almost exclusively of such genes. Among these regions were six that included previously identified cryptic phage. A hypothetical ancestral state of genomic regions that differ between ECO and SAL can be inferred in some cases by reference to the genome structure in KPN and the more distant relative Yersinia pestis. However, many changes between ECO and SAL are concentrated in regions where all four genera have a different structure. The rate of gene insertion and deletion is sufficiently high in these regions that the ancestral state of the ECO/SAL lineage cannot be inferred from the present data. The sequencing of other closely related genomes, such as S.bongori or Citrobacter, may help in this regard.
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Affiliation(s)
- M McClelland
- Sidney Kimmel Cancer Center, 10835 Altman Row, San Diego, CA 92121, USA
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Abstract
This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715-1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included.
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Affiliation(s)
- M K Berlyn
- Department of Biology and School of Forestry and Environmental Studies, Yale University, New Haven, Connecticut 06520-8104, USA.
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French C, Ward JM. Production and modification of E. coli transketolase for large-scale biocatalysis. Ann N Y Acad Sci 1996; 799:11-8. [PMID: 8958067 DOI: 10.1111/j.1749-6632.1996.tb33171.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- C French
- Department of Biochemistry and Molecular Biology, University College London, United Kingdom
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Henstra SA, Tolner B, ten Hoeve Duurkens RH, Konings WN, Robillard GT. Cloning, expression, and isolation of the mannitol transport protein from the thermophilic bacterium Bacillus stearothermophilus. J Bacteriol 1996; 178:5586-91. [PMID: 8824601 PMCID: PMC178395 DOI: 10.1128/jb.178.19.5586-5591.1996] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
A mannitol phosphotransferase system (PTS) was identified in Bacillus stearothermophilus by in vitro complementation with Escherichia coli EI, HPr, and IIA(Mtl). Degenerate primers based on regions of high amino acid similarity in the E. coli and Staphylococcus carnosus EII(Mt1) were used to develop a digoxigenin-labeled probe by PCR. Using this probe, we isolated three overlapping DNA fragments totaling 7.2 kb which contain the genes mtlA, mtlR, mtlF, and mtlD, encoding the mannitol IICB,a regulator, IIA, and a mannitol-1-phosphate dehydrogenase, respectively. The mtl4 gene consists of 1,413 bp coding for a 471-amino-acid protein with a calculated mass of 50.1 kDa. The amino acid sequence shows high similarity with the sequence of IICB(Mtl) of S. carnosus and the IICB part of the IICBA(Mtl)s of E. coli and B. subtilis. The enzyme could be functionally expressed in E. coli by placing it behind the strong tac promoter. The rate of thermal inactivation at 60 degrees C of B. stearothermophilus HCB(Mt1) expressed in E. coli was two times lower than that of E. coli IICB(Mtl). IICB(Mtl) in B. stearothermophilus is maximally active at 85 degrees C and thus very thermostable. The enzyme was purified on Ni-nitrilotriacetic acid resin to greater than 95% purity after six histidines were fused to the C-terminal part of the transporter.
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Affiliation(s)
- S A Henstra
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
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11
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REIZER JONATHAN, CHARBIT ALAIN, REIZER AIALA, SAIER MILTONH. Novel Phosphotransferase System Genes Revealed by Bacterial Genome Analysis: Operons Encoding Homologues of Sugar-Specific Permease Domains of the Phosphotransferase System and Pentose Catabolic Enzymes. ACTA ACUST UNITED AC 1996. [DOI: 10.1089/gst.1996.1.53] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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12
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Powell BS, Court DL, Inada T, Nakamura Y, Michotey V, Cui X, Reizer A, Saier MH, Reizer J. Novel proteins of the phosphotransferase system encoded within the rpoN operon of Escherichia coli. Enzyme IIANtr affects growth on organic nitrogen and the conditional lethality of an erats mutant. J Biol Chem 1995; 270:4822-39. [PMID: 7876255 DOI: 10.1074/jbc.270.9.4822] [Citation(s) in RCA: 177] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Two rpoN-linked delta Tn10-kan insertions suppress the conditionally lethal erats allele. One truncates rpoN while the second disrupts another gene (ptsN) in the rpoN operon and does not affect classical nitrogen regulation. Neither alter expression of era indicating that suppression is post-translational. Plasmid clones of ptsN prevent suppression by either disruption mutation indicating that this gene is important for lethality caused by erats. rpoN and six neighboring genes were sequenced and compared with sequences in the database. Two of these genes encode proteins homologous to Enzyme IIAFru and HPr of the phosphoenolpyruvate:sugar phosphotransferase system. We designate these proteins IIANtr (ptsN) and NPr (npr). Purified IIANtr and NPr exchange phosphate appropriately with Enzyme I, HPr, and Enzyme IIA proteins of the phosphoenolpyruvate: sugar phosphotransferase system. Several sugars and tricarboxylic acid cycle intermediates inhibited growth of the ptsN disruption mutant on medium containing an amino acid or nucleoside base as a combined source of nitrogen, carbon, and energy. This growth inhibition was relieved by supplying the ptsN gene or ammonium salts but was not aleviated by altering levels of exogenously supplied cAMP. These results support our previous proposal of a novel mechanism linking carbon and nitrogen assimilation and relates IIANtr to the unknown process regulated by the essential GTPase Era.
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Affiliation(s)
- B S Powell
- Laboratory of Chromosome Biology, NCI-Frederick Cancer Research and Development Center, Maryland 21702-1201
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13
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Improved production and stability ofE. coli recombinants expressing transketolase for large scale biotransformation. Biotechnol Lett 1995. [DOI: 10.1007/bf01190631] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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14
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Stojiljkovic I, Bäumler AJ, Heffron F. Ethanolamine utilization in Salmonella typhimurium: nucleotide sequence, protein expression, and mutational analysis of the cchA cchB eutE eutJ eutG eutH gene cluster. J Bacteriol 1995; 177:1357-66. [PMID: 7868611 PMCID: PMC176743 DOI: 10.1128/jb.177.5.1357-1366.1995] [Citation(s) in RCA: 275] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
A fragment of the Salmonella typhimurium ethanolamine utilization operon was cloned and characterized. The 6.3-kb nucleotide sequence encoded six complete open reading frames, termed cchA, cchB, eutE, eutJ, eutG, and eutH. In addition, the nucleotide sequences of two incomplete open reading frames, termed eutX and eutI, were also determined. Comparison of the deduced amino acid sequences and entries in the GenBank database indicated that eutI encodes a phosphate acetyltransferase-like enzyme. The deduced amino acid sequences of the EutE and EutG proteins revealed a significant degree of homology with the Escherichia coli alcohol dehydrogenase AdhE sequence. Mutations in eutE or eutG completely abolished the ability of mutants to utilize ethanolamine as a carbon source and reduced the ability to utilize ethanolamine as a nitrogen source. The product of eutE is most probably an acetaldehyde dehydrogenase catalyzing the conversion of acetaldehyde into acetyl coenzyme A. The product of the eutG gene, an uncommon iron-containing alcohol dehydrogenase, may protect the cell from unconverted acetaldehyde by converting it into an alcohol. The deduced amino acid sequence of cchA resembles that of carboxysome shell proteins from Thiobacillus neapolitanus and Synechococcus sp. as well as that of the PduA product from S. typhimurium. CchA and CchB proteins may be involved in the formation of an intracellular microcompartment responsible for the metabolism of ethanolamine. The hydrophobic protein encoded by the eutH gene possesses some characteristics of bacterial permeases and might therefore be involved in the transport of ethanolamine. Ethanolamine-utilization mutants were slightly attenuated in a mouse model of S. typhimurium infection, indicating that ethanolamine may be an important source of nitrogen and carbon for S. typhimurium in vivo.
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Affiliation(s)
- I Stojiljkovic
- Department of Microbiology and Immunology, Oregon Health Sciences University, Portland 97201
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Lengeler JW, Jahreis K, Wehmeier UF. Enzymes II of the phospho enol pyruvate-dependent phosphotransferase systems: their structure and function in carbohydrate transport. BIOCHIMICA ET BIOPHYSICA ACTA 1994; 1188:1-28. [PMID: 7947897 DOI: 10.1016/0005-2728(94)90017-5] [Citation(s) in RCA: 102] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- J W Lengeler
- Arbeitsgruppe Genetik, Fachbereich Biologie/Chemie, Universität Osnabrück, Germany
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Metzger MH, Hollenberg CP. Isolation and characterization of the Pichia stipitis transketolase gene and expression in a xylose-utilising Saccharomyces cerevisiae transformant. Appl Microbiol Biotechnol 1994; 42:319-25. [PMID: 7765773 DOI: 10.1007/bf00902736] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The gene TKT from P. stipitis, encoding the enzyme transketolase (EC 2.2.1.1), was cloned from a genomic library by hybridization with a S. cerevisiae TKT1-gene-specific probe. The nucleotide sequence determined contains an open-reading frame of 2085 base pairs (bp) encoding a protein of 695 amino acids with a predicted molecular mass of 75113 Da. The TKT gene was actively expressed in S. cerevisiae when placed under the control of the homologous PDC1(-15) promoter and could complement a S. cerevisiae tkt deletion. The TKT protein was immunologically detectable using S. cerevisiae transketolase-specific antiserum. Overexpression of the P. stipitis TKT gene in a xylose-utilizing S. cerevisiae XYL1/XYL2 integrant led to a drastically extended generation time during growth on xylose minimal medium under aerobic conditions.
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Affiliation(s)
- M H Metzger
- Institut für Mikrobiologie, Heinrich-Heine-Universität, Düsseldorf, Germany
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17
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Abstract
In 1964, Kundig, Ghosh and Roseman reported the discovery of the phosphoenolpyruvate:sugar phosphotransferase system (PTS). Thirty years later, we find that the PTS functions not only as a sugar-phosphorylating system, but also as a complex protein kinase system that regulates a wide variety of metabolic processes and controls the expression of numerous genes. As a result of recent operon- and genome-sequencing projects, novel PTS protein-encoding genes have been discovered, most of which have yet to be functionally defined. Some of them appear to be involved in cellular processes distinct from those recognized previously. Fundamental aspects of past and current PTS research are briefly reviewed, and recent advances are integrated into conceptual pictures that provide guides for future research.
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Affiliation(s)
- M H Saier
- Department of Biology, University of California at San Diego, La Jolla 92093-0116
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18
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Reizer J, Michotey V, Reizer A, Saier MH. Novel phosphotransferase system genes revealed by bacterial genome analysis: unique, putative fructose- and glucoside-specific systems. Protein Sci 1994; 3:440-50. [PMID: 8019415 PMCID: PMC2142697 DOI: 10.1002/pro.5560030309] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Analyses of sequences made available through the Escherichia coli genome project in the 87.2-89.2-min and 81.5-84.5-min regions have revealed 2 putative operons encoding proteins of the phosphoenolpyruvate:sugar phosphotransferase system (PTS). The first putative operon, designated frv, includes 4 open reading frames (ORFs), ORFf147, ORFf485, ORFf356, and ORFf582, ORFf147 and ORFf485 comprise an Enzyme IIA-Enzyme IIBC pair of the PTS. The sequence similarity of ORFf485 to previously characterized fructose-specific Enzymes IIBC suggests that ORFf485 may be specific for fructose. ORFf147 encodes a protein with comparable degrees of sequence similarity to fructose and mannitol-specific Enzymes IIA as well as homologous proteins implicated in sigma 54-dependent transcriptional regulation. Unique features of this system include a detached IIA protein and the absence of a IIB domain duplication. ORFf356 and ORFf582 are functionally unidentified and nonhomologous to other ORFs in the current protein databases, but ORFf582 contains 2 N-terminal helix-turn-helix motifs, suggestive of a role in frv operon transcriptional regulation. The second putative operon, designated glv, includes 3 ORFs, ORFf455, ORFf161, and ORFf212. We suggest that ORFf455 was incorrectly assigned and should be designated ORFf368. ORFf368 and ORFf161 encode an Enzyme IIC and IIB pair of the PTS showing greatest sequence similarity to Enzymes II specific for sugars of the gluco configuration. ORFf212 encodes a protein with sequence similarity to a phospho-beta-glucosidase and an alpha-galactosidase. No putative transcriptional regulator of the glv operon was found. This operon is the first one encoding a putative PTS permease with detached Enzymes IIB and IIC and lacking an Enzyme IIA. It is suggested that both the frv and glv operons are cryptic in E. coli and that additional genes encoding novel PTS-related proteins will be revealed by bacterial genome sequence analyses.
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Affiliation(s)
- J Reizer
- Department of Biology, University of California at San Diego, La Jolla 92093-0116
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19
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Sprenger GA. Nucleotide sequence of the Escherichia coli K-12 transketolase (tkt) gene. BIOCHIMICA ET BIOPHYSICA ACTA 1993; 1216:307-10. [PMID: 8241274 DOI: 10.1016/0167-4781(93)90161-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The gene tkt for the enzyme transketolase (TK; EC 2.2.1.1) of Escherichia coli K-12 was subcloned and the complete DNA sequence was determined from both strands. An open reading frame with 1992 bp was detected that could encode a protein with a subunit mass of 72,143. The gene forms a monocistronic operon and is transcribed counterclockwise to the E. coli chromosome. From recombinant strains, the enzyme was purified and 39 N-terminal amino acid residues were determined. The DNA-derived protein sequence showed 49.5% identical amino acid residues with the transketolase of Rhodobacter sphaeroides, 46.8% identity with the enzyme from Saccharomyces cerevisiae, and 28.9% identity with the human transketolase.
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Affiliation(s)
- G A Sprenger
- Forschungszentrum Jülich GmbH, Institut für Biotechnologie 1, Jülich, Germany
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